Hi, You can try swissparam online tool to generate protein and ligand topologies..
Cheers, Nitin On Wed, Nov 16, 2011 at 7:03 AM, arun kumar <[email protected]>wrote: > hi justin, > > as u said i understand that there is inconsistency in the charges and > charge groups of PRODRG server itself. > can u suggest me any other softwares that i can rely on for this work. > > Thanking you. > > On Tue, Nov 15, 2011 at 7:48 PM, <[email protected]> wrote: > >> Send gmx-users mailing list submissions to >> [email protected] >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> or, via email, send a message with subject or body 'help' to >> [email protected] >> >> You can reach the person managing the list at >> [email protected] >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of gmx-users digest..." >> >> >> Today's Topics: >> >> 1. Re: ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION (Justin A. Lemkul) >> 2. RMSD (shahid nayeem) >> 3. Problem during GROMACS 4.5.5 installation (sai nitin) >> 4. Re: Problem during GROMACS 4.5.5 installation (Justin A. Lemkul) >> 5. Re: RMSD (Gianluca Santoni) >> 6. Re: RMSD ([email protected]) >> 7. Re: Positive potential energy for TFE solvent (Harpreet Basra) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 15 Nov 2011 06:40:31 -0500 >> From: "Justin A. Lemkul" <[email protected]> >> Subject: Re: [gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION >> To: Discussion list for GROMACS users <[email protected]> >> Message-ID: <[email protected]> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> >> >> arun kumar wrote: >> > Dear friends, >> > >> > i had a problem while running the of protein-ligand complex simulation, >> > in which i have generated the ligand toplogy by using online Prodrg >> > server and iam using gromos 96.1froce field. >> > >> > there was an note and an error during minimization >> > >> > NOTE 2 [file trp.top]: >> > The largest charge group contains 15 atoms. >> > Since atoms only see each other when the centers of geometry of the >> charge >> > groups they belong to are within the cut-off distance, too large >> charge >> > groups can lead to serious cut-off artifacts. >> > For efficiency and accuracy, charge group should consist of a few >> atoms. >> > For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, >> etc. >> > >> > Analysing residue names: >> > There are: 223 Protein residues >> > There are: 1 Other residues >> > There are: 25853 Water residues >> > Analysing Protein... >> > Analysing residues not classified as Protein/DNA/RNA/Water and splitting >> > into groups... >> > Number of degrees of freedom in T-Coupling group rest is 161838.00 >> > Largest charge group radii for Van der Waals: 0.790, 0.356 nm >> > Largest charge group radii for Coulomb: 0.790, 0.399 nm >> > >> > WARNING 1 [file em.mdp]: >> > The sum of the two largest charge group radii (1.188798) is larger >> than >> > rlist (1.000000) >> > >> > i am using the mdp file the one that i copied from gromacs >> > protein-ligand tutorial >> > >> > can any one please explain these errors so that i can go farward in my >> work. >> > >> >> >> http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb >> >> > and i have a doubt, as there are other updated forcefields, how much >> > reliable is the gromos 96 ff.... >> > >> >> The problem is not the reliability of Gromos96, but the reliability of >> PRODRG. >> Please read the paper linked from >> http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips to >> understand why >> you should almost certainly never use the charges and charge groups that >> PRODRG >> creates. >> >> -Justin >> >> -- >> ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> >> >> ------------------------------ >> >> Message: 2 >> Date: Tue, 15 Nov 2011 17:53:19 +0530 >> From: shahid nayeem <[email protected]> >> Subject: [gmx-users] RMSD >> To: Discussion list for GROMACS users <[email protected]> >> Message-ID: >> <CAB_3DJa8m-jooJb= >> [email protected]> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Dear all >> I am interested to get contour plot of residue RMSD vs time graph. I want >> to get the flexible and rigid regions of protein chain during simulation. >> g_rmsf does not gives me this plot. >> Please help >> shahid Nayeem >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://lists.gromacs.org/pipermail/gmx-users/attachments/20111115/c99194fb/attachment-0001.html >> >> ------------------------------ >> >> Message: 3 >> Date: Tue, 15 Nov 2011 14:03:03 +0100 >> From: sai nitin <[email protected]> >> Subject: [gmx-users] Problem during GROMACS 4.5.5 installation >> To: [email protected] >> Message-ID: >> < >> cagjtc4nwdf9a2v9t8eep1jma+s4kecoa6p8rnl6vnm_m7hq...@mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi all, >> >> >> I just started learning molecular dynamics analysis of protein-ligand >> complexes to do this i downloaded GROMACS 4.5.5 and tried to install >> according to Manual instructions executed following commands.. >> >> ./configure >> make (when i executed this command it is showing following error *** No >> targets specified and no makefile found) >> >> Can any body help how to solved this... >> >> Thanks in advance >> -- >> >> Sainitin D >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://lists.gromacs.org/pipermail/gmx-users/attachments/20111115/ab159056/attachment-0001.html >> >> ------------------------------ >> >> Message: 4 >> Date: Tue, 15 Nov 2011 08:13:40 -0500 >> From: "Justin A. Lemkul" <[email protected]> >> Subject: Re: [gmx-users] Problem during GROMACS 4.5.5 installation >> To: Discussion list for GROMACS users <[email protected]> >> Message-ID: <[email protected]> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> >> >> sai nitin wrote: >> > Hi all, >> > >> > >> > I just started learning molecular dynamics analysis of protein-ligand >> > complexes to do this i downloaded GROMACS 4.5.5 and tried to install >> > according to Manual instructions executed following commands.. >> > >> > ./configure >> > make (when i executed this command it is showing following error *** No >> > targets specified and no makefile found) >> > >> >> Configuration failed. Simply specifying ./configure without any options >> is >> often insufficient. Please follow the installation guide online. >> >> -Justin >> >> -- >> ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> >> >> ------------------------------ >> >> Message: 5 >> Date: Tue, 15 Nov 2011 21:18:16 +0800 >> From: Gianluca Santoni <[email protected]> >> Subject: Re: [gmx-users] RMSD >> To: Discussion list for GROMACS users <[email protected]> >> Message-ID: <[email protected]> >> Content-Type: text/plain; charset="iso-8859-1" >> >> On 11/15/11 8:23 PM, shahid nayeem wrote: >> > Dear all >> > I am interested to get contour plot of residue RMSD vs time graph. I >> > want to get the flexible and rigid regions of protein chain during >> > simulation. g_rmsf does not gives me this plot. >> > Please help >> > shahid Nayeem >> > >> > >> > >> Try g_rmsf -res , it could be useful, maybe. >> >> -- >> Gianluca Santoni, >> Institut de Biologie Structurale >> 41 rue Horowitz >> Grenoble >> _________________________________________________________ >> Please avoid sending me Word or PowerPoint attachments. >> See http://www.gnu.org/philosophy/no-word-attachments.html >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://lists.gromacs.org/pipermail/gmx-users/attachments/20111115/fae5e453/attachment-0001.html >> >> ------------------------------ >> >> Message: 6 >> Date: Tue, 15 Nov 2011 10:32:16 -0300 (GMT-03:00) >> From: "[email protected]" <[email protected]> >> Subject: Re: [gmx-users] RMSD >> To: <[email protected]> >> Message-ID: >> <10450993.2631321363936014.JavaMail.defaultUser@defaultHost> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> In any case, if you really want to see flexibility then you need RMSF and >> not RMSD as the later will only tell you about how similar is the >> configuration of a sidechain compared to a reference frame. If that is >> still what you want i think VMD has a tool for that in the timeline plugin. >> >> >> >> regards >> >> >> >> Felipe >> ----Mensaje original---- De: [email protected] Fecha: 15-nov-2011 >> 10:18 Para: "Discussion list for GROMACS users"<[email protected]> >> Asunto: Re: [gmx-users] RMSD On 11/15/11 8:23 PM, shahid nayeem wrote: >> Dear all >> I am interested to get contour plot of residue RMSD vs time >> graph. I want to get the flexible and rigid regions of protein >> chain during simulation. g_rmsf does not gives me this plot. >> Please help >> shahid Nayeem >> >> >> Try g_rmsf -res , it could be useful, maybe. >> -- >> Gianluca Santoni, >> Institut de Biologie Structurale >> 41 rue Horowitz >> Grenoble >> _________________________________________________________ >> Please avoid sending me Word or PowerPoint attachments. >> See http://www.gnu.org/philosophy/no-word-attachments.html >> >> >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://lists.gromacs.org/pipermail/gmx-users/attachments/20111115/fb43cbe3/attachment-0001.html >> >> ------------------------------ >> >> Message: 7 >> Date: Tue, 15 Nov 2011 19:48:06 +0530 >> From: Harpreet Basra <[email protected]> >> Subject: [gmx-users] Re: Positive potential energy for TFE solvent >> To: [email protected] >> Message-ID: >> < >> caeaim5ssflvhhe+zm1z60t4b-bkuj5vcpbefza92g255qy2...@mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi Mark, >> >> Thanks for the quick reply. But i have already done what u suggested. >> >> >> > >> > On 15/11/2011 6:06 PM, Harpreet Basra wrote: >> > > Hi >> > > I am still stuck with same problem of obtaining positive potential >> > > energy. >> > > >>On 11/11/2011 5:07 PM, Harpreet Basra wrote: >> > > >> Hi >> > > >> >> > > >> I am trying to generate an equilibrated box of 216 TFE molecules.To >> > > >> generate the 216 TFE molecule box i performed following steps: >> > > > >> > > >A suggested workflow can be found here >> > > >http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation >> > > I have been following this link only. >> > > > >> > > > >> > > >> 1) I got the tfe.gro file and created a cubic box of edge length = >> > > >> 0.516 nm containing 1 TFE molecule (at its center), using the >> > > >> following command: >> > > >> >> > > >>>> editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516 >> > > >> I chose this length because in the tfe.gro file dimensions of the >> TFE >> > > >> molecule are 0.516 0.516 0.516. >> > > > >> > > >That's not a good reason. Choose a volume and shape that makes sense >> for >> > > >your target density. Cubic probably doesn't make sense when a >> > > >rectangular shape is possible. Then you'll probably want to choose >> -nbox >> > > >differently later. >> > > I chose a rectangular box too. still i get a positive value for PE and >> > > moreover all the molecules move towards two opposite walls of the box. >> > > I am not sure that the way I am using the genconf command is the >> > > correct way. because I have tried every other possibility for not >> > > getting a positive potential, with no success. So here are my .gro >> > > file and the topology file for TFE. >> > > *****tfe.gro file***** >> > > 7 >> > > >> > > 1TFE F1T 1 0.444 0.344 0.246 >> > > >> > > 1TFE CT 2 0.334 0.245 0.246 >> > > >> > > 1TFE F2T 3 0.350 0.160 0.364 >> > > >> > > 1TFE F3T 4 0.350 0.160 0.127 >> > > >> > > 1TFE CH2T 5 0.187 0.326 0.246 >> > > >> > > 1TFE OT 6 0.075 0.220 0.246 >> > > >> > > 1TFE HT 7 -0.019 0.266 0.246 >> > > >> > > 0.49174 0.49174 0.49174 >> > > >> > > ****topology file**** >> > > >> > > [ moleculetype ] >> > > >> > > ; Name nrexcl >> > > >> > > TFE 3 >> > > >> > > [ atoms ] >> > > >> > > ; nr type resnr resid atom cgnr charge mass >> > > >> > > 1 FTFE 1 TFE F1T 1 -0.170 18.9984 >> > > >> > > 2 CTFE 1 TFE CT 1 0.452 12.0110 >> > > >> > > 3 FTFE 1 TFE F2T 1 -0.170 18.9984 >> > > >> > > 4 FTFE 1 TFE F3T 1 -0.170 18.9984 >> > > >> > > 5 CHTFE 1 TFE CH2T 1 0.273 14.0270 >> > > >> > > 6 OTFE 1 TFE OT 1 -0.625 15.9994 >> > > >> > > 7 H 1 TFE HT 1 0.410 1.0080 >> > > >> > > [ bonds ] >> > > >> > > ; ai aj fu c0, c1, ... >> > > >> > > 2 1 2 0.133 3380866.9 0.133 3380866.9 ; C1 F1 >> > > >> > > 2 3 2 0.133 3380866.9 0.133 3380866.9 ; C1 F2 >> > > >> > > 2 4 2 0.133 3380866.9 0.133 3380866.9 ; C1 F3 >> > > >> > > 2 5 2 0.153 7150000.0 0.153 7150000.0 ; C1 C2 >> > > >> > > 5 6 2 0.143 8180000.0 0.143 8180000.0 ; C2 O >> > > >> > > 6 7 2 0.100 15700000.0 0.100 15700000.0 ; O H >> > > >> > > [ pairs ] >> > > >> > > ; ai aj fu c0, c1, ... >> > > >> > > 1 6 1 ; F1 O >> > > >> > > 2 7 1 ; C1 H >> > > >> > > 3 6 1 ; F2 O >> > > >> > > 4 6 1 ; F3 O >> > > >> > > [ angles ] >> > > >> > > ; ai aj ak fu c0, c1, ... >> > > >> > > 1 2 3 2 109.5 520.0 109.5 520.0 ; F1 C1 F2 >> > > >> > > 1 2 4 2 109.5 520.0 109.5 520.0 ; F1 C1 F3 >> > > >> > > 1 2 5 2 109.5 520.0 109.5 520.0 ; F1 C1 C2 >> > > >> > > 3 2 4 2 109.5 520.0 109.5 520.0 ; F2 C1 F3 >> > > >> > > 3 2 5 2 109.5 520.0 109.5 520.0 ; F2 C1 C2 >> > > >> > > 4 2 5 2 109.5 520.0 109.5 520.0 ; F3 C1 C2 >> > > >> > > 2 5 6 2 109.5 520.0 109.5 520.0 ; C1 C2 O >> > > >> > > 5 6 7 2 109.5 450.0 109.5 450.0 ; C2 O H >> > > >> > > [ dihedrals ] >> > > >> > > ; ai aj ak al fu c0, c1, m, ... >> > > >> > > 6 5 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih O C2 C1 F1 >> > > >> > > 2 5 6 7 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2 O H >> > > >> > > and to construct a box of TFE solvent i took the tfe.gro file and >> > > replicated the TFE molecule by using >> > > genconf -f tfe.gro -o tfe_sol.gro -rot -nbox 6 >> > > can u plz suggest is it that I am using genconf in a wrong way that it >> > > is causing this problem? I am not sure how many molecules (-nbox >> > > option in genconf) should i keep in the box in order to get a mass >> > > density of 1383g/L for TFE. >> > >> > That link says "Work out how much volume a single molecule would have in >> > the box of your chosen density and size. Useeditconf >> > <http://www.gromacs.org/editconf>to place a box of that size around >> your >> > single molecule." It does not seem to me that you have done this. >> > >> > Mark >> > >> >> I did place the *single molecule* in a box of size required to get a >> density of 1383 g/L. I also checked the density of the solvent box >> (containing 216 molecules after NVT equilibration for 200 ps) I >> constructed >> the average value comes out to be 1397 g/L with a std deviation of 30 g/L, >> thus it seems range. Moreover, the potential energy of this one molecule >> (tfe.gro) was coming out to be highly negative (-6.4E+08 kJ/mol). But on >> generating a solvent system with 216 TFE molecules the energy becomes >> (1.9E+04 kJ/mol). >> >> Harpreet >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://lists.gromacs.org/pipermail/gmx-users/attachments/20111115/87c00073/attachment.html >> >> ------------------------------ >> >> -- >> gmx-users mailing list >> [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> >> End of gmx-users Digest, Vol 91, Issue 104 >> ****************************************** >> > > > > -- > Arun Kumar Somavarapu > Project-JRF > Dr. Prasanna's lab > TMC, ACTREC > Navi Mumbai-410210 > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Sainitin D PhD student Bioinformatics Group Biotechnology Center Technische Universität Dresden Tatzberg 47/49 01307 Dresden, Germany Tel Lab:+49 (0)351 463 40060
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